Starting phenix.real_space_refine on Fri Jun 13 17:16:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wda_37459/06_2025/8wda_37459.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wda_37459/06_2025/8wda_37459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wda_37459/06_2025/8wda_37459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wda_37459/06_2025/8wda_37459.map" model { file = "/net/cci-nas-00/data/ceres_data/8wda_37459/06_2025/8wda_37459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wda_37459/06_2025/8wda_37459.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3598 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 7897 2.51 5 N 2205 2.21 5 O 2231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12359 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3962 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 41, 'TRANS': 475} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2233 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 1 Chain: "C" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2123 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 269} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 23 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "D" Number of atoms: 3975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3975 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 27, 'TRANS': 496} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'9XX': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 8.04, per 1000 atoms: 0.65 Number of scatterers: 12359 At special positions: 0 Unit cell: (86.92, 94.3, 164.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 2231 8.00 N 2205 7.00 C 7897 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.5 seconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 11 sheets defined 48.0% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.704A pdb=" N THR A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 4.865A pdb=" N ILE A 59 " --> pdb=" O ASN A 55 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 121 removed outlier: 3.787A pdb=" N PHE A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 178 through 182 removed outlier: 4.203A pdb=" N GLY A 181 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 195 through 200 removed outlier: 3.608A pdb=" N PHE A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 200 " --> pdb=" O MET A 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 200' Processing helix chain 'A' and resid 252 through 263 Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.809A pdb=" N LEU A 276 " --> pdb=" O PRO A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 319 through 322 removed outlier: 3.598A pdb=" N ALA A 322 " --> pdb=" O LEU A 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 319 through 322' Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.592A pdb=" N GLN A 330 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 377 removed outlier: 3.731A pdb=" N ARG A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 421 through 431 removed outlier: 6.240A pdb=" N THR A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 490 through 504 removed outlier: 3.719A pdb=" N ARG A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 29 removed outlier: 4.166A pdb=" N ALA B 6 " --> pdb=" O GLY B 2 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG B 7 " --> pdb=" O TRP B 3 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 10 " --> pdb=" O ALA B 6 " (cutoff:3.500A) Proline residue: B 14 - end of helix removed outlier: 3.967A pdb=" N LEU B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 49 through 53 removed outlier: 3.709A pdb=" N ARG B 53 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 75 removed outlier: 3.533A pdb=" N GLN B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 104 Proline residue: B 96 - end of helix removed outlier: 3.813A pdb=" N ILE B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.949A pdb=" N ILE B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 140 removed outlier: 3.581A pdb=" N ILE B 140 " --> pdb=" O GLY B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.694A pdb=" N GLY B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 202 removed outlier: 3.599A pdb=" N ALA B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.886A pdb=" N ARG B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 230 through 240 Processing helix chain 'B' and resid 240 through 255 removed outlier: 3.664A pdb=" N GLY B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 250 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B 254 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 270 Processing helix chain 'B' and resid 273 through 302 removed outlier: 3.756A pdb=" N VAL B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 307 removed outlier: 3.605A pdb=" N ARG B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 307' Processing helix chain 'C' and resid 7 through 16 removed outlier: 3.863A pdb=" N ALA C 11 " --> pdb=" O PHE C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 37 removed outlier: 3.673A pdb=" N ALA C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 41 Processing helix chain 'C' and resid 72 through 106 removed outlier: 3.591A pdb=" N ARG C 76 " --> pdb=" O ASP C 72 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY C 80 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA C 94 " --> pdb=" O GLY C 90 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 128 through 139 removed outlier: 3.549A pdb=" N ALA C 132 " --> pdb=" O PRO C 128 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 157 removed outlier: 3.693A pdb=" N PHE C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TRP C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.533A pdb=" N GLU C 170 " --> pdb=" O GLY C 166 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 186 through 196 Processing helix chain 'C' and resid 201 through 224 removed outlier: 4.031A pdb=" N VAL C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 224 " --> pdb=" O THR C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 253 through 279 removed outlier: 3.595A pdb=" N ALA C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 57 removed outlier: 3.770A pdb=" N THR D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 88 removed outlier: 3.629A pdb=" N ARG D 86 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 116 Processing helix chain 'D' and resid 130 through 138 removed outlier: 3.682A pdb=" N LEU D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 149 removed outlier: 3.739A pdb=" N ARG D 149 " --> pdb=" O GLN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 168 removed outlier: 3.714A pdb=" N GLN D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 165 " --> pdb=" O ARG D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 200 removed outlier: 3.834A pdb=" N GLN D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D 193 " --> pdb=" O GLN D 189 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY D 198 " --> pdb=" O ASP D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 247 through 255 Processing helix chain 'D' and resid 257 through 262 removed outlier: 3.729A pdb=" N THR D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 339 removed outlier: 3.609A pdb=" N ARG D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 338 " --> pdb=" O ALA D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 393 removed outlier: 3.566A pdb=" N ILE D 392 " --> pdb=" O VAL D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 399 removed outlier: 3.966A pdb=" N HIS D 399 " --> pdb=" O PRO D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 418 removed outlier: 3.530A pdb=" N ARG D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL D 411 " --> pdb=" O ARG D 407 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP D 416 " --> pdb=" O ARG D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 433 removed outlier: 3.508A pdb=" N GLU D 431 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU D 432 " --> pdb=" O PRO D 429 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER D 433 " --> pdb=" O ARG D 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 428 through 433' Processing helix chain 'D' and resid 437 through 446 removed outlier: 3.668A pdb=" N ALA D 441 " --> pdb=" O ARG D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 475 removed outlier: 3.648A pdb=" N ALA D 468 " --> pdb=" O VAL D 464 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN D 469 " --> pdb=" O LEU D 465 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP D 472 " --> pdb=" O ALA D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 480 removed outlier: 3.884A pdb=" N ALA D 479 " --> pdb=" O ALA D 475 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP D 480 " --> pdb=" O ASP D 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 475 through 480' Processing helix chain 'D' and resid 531 through 535 removed outlier: 3.858A pdb=" N ALA D 534 " --> pdb=" O LEU D 531 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE D 535 " --> pdb=" O LEU D 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 531 through 535' Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 70 Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 86 removed outlier: 4.025A pdb=" N SER A 83 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 268 Processing sheet with id=AA6, first strand: chain 'A' and resid 267 through 268 removed outlier: 6.808A pdb=" N GLN A 296 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASP A 511 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE A 294 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE A 513 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA A 292 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL A 515 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLY A 290 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLY A 517 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THR A 288 " --> pdb=" O GLY A 517 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP A 442 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASN A 390 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 11.324A pdb=" N GLY A 441 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR A 385 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ALA A 417 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE A 387 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLN A 419 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR A 389 " --> pdb=" O GLN A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 12 through 18 removed outlier: 7.080A pdb=" N GLY D 13 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY D 68 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU D 15 " --> pdb=" O THR D 66 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR D 17 " --> pdb=" O ARG D 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 94 through 96 removed outlier: 3.854A pdb=" N GLU D 234 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ARG D 228 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 71 through 72 removed outlier: 3.732A pdb=" N ARG D 75 " --> pdb=" O PHE D 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 282 through 293 removed outlier: 7.098A pdb=" N VAL D 283 " --> pdb=" O ARG D 313 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ARG D 313 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER D 285 " --> pdb=" O SER D 311 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER D 311 " --> pdb=" O SER D 285 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU D 287 " --> pdb=" O GLY D 309 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 307 " --> pdb=" O LYS D 289 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR D 291 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ARG D 305 " --> pdb=" O TYR D 291 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLU D 293 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU D 303 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 372 through 374 removed outlier: 7.390A pdb=" N GLN D 372 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ASP D 456 " --> pdb=" O GLN D 372 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL D 374 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU D 453 " --> pdb=" O LEU D 486 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE D 488 " --> pdb=" O LEU D 453 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS D 455 " --> pdb=" O ILE D 488 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA D 321 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N MET D 505 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL D 323 " --> pdb=" O MET D 505 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL D 502 " --> pdb=" O HIS D 513 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N HIS D 513 " --> pdb=" O VAL D 502 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL D 504 " --> pdb=" O VAL D 511 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2013 1.31 - 1.43: 3302 1.43 - 1.56: 7258 1.56 - 1.68: 0 1.68 - 1.81: 47 Bond restraints: 12620 Sorted by residual: bond pdb=" CA ALA D 257 " pdb=" C ALA D 257 " ideal model delta sigma weight residual 1.527 1.474 0.053 1.31e-02 5.83e+03 1.63e+01 bond pdb=" O 9XX A 602 " pdb=" C15 9XX A 602 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C18 9XX A 602 " pdb=" O1 9XX A 602 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" N ALA D 257 " pdb=" CA ALA D 257 " ideal model delta sigma weight residual 1.458 1.416 0.042 1.48e-02 4.57e+03 8.02e+00 bond pdb=" CA PRO D 258 " pdb=" CB PRO D 258 " ideal model delta sigma weight residual 1.534 1.499 0.035 1.40e-02 5.10e+03 6.10e+00 ... (remaining 12615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 16932 2.41 - 4.83: 236 4.83 - 7.24: 38 7.24 - 9.65: 3 9.65 - 12.07: 1 Bond angle restraints: 17210 Sorted by residual: angle pdb=" N VAL A 90 " pdb=" CA VAL A 90 " pdb=" C VAL A 90 " ideal model delta sigma weight residual 113.71 108.42 5.29 9.50e-01 1.11e+00 3.10e+01 angle pdb=" N ALA D 257 " pdb=" CA ALA D 257 " pdb=" C ALA D 257 " ideal model delta sigma weight residual 110.07 104.31 5.76 1.26e+00 6.30e-01 2.09e+01 angle pdb=" N ARG B 7 " pdb=" CA ARG B 7 " pdb=" C ARG B 7 " ideal model delta sigma weight residual 113.41 108.35 5.06 1.22e+00 6.72e-01 1.72e+01 angle pdb=" N VAL A 80 " pdb=" CA VAL A 80 " pdb=" C VAL A 80 " ideal model delta sigma weight residual 111.90 108.80 3.10 8.10e-01 1.52e+00 1.47e+01 angle pdb=" N LEU B 215 " pdb=" CA LEU B 215 " pdb=" C LEU B 215 " ideal model delta sigma weight residual 110.35 115.67 -5.32 1.40e+00 5.10e-01 1.45e+01 ... (remaining 17205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.47: 7355 34.47 - 68.93: 127 68.93 - 103.40: 12 103.40 - 137.87: 3 137.87 - 172.33: 1 Dihedral angle restraints: 7498 sinusoidal: 2875 harmonic: 4623 Sorted by residual: dihedral pdb=" C THR D 261 " pdb=" N THR D 261 " pdb=" CA THR D 261 " pdb=" CB THR D 261 " ideal model delta harmonic sigma weight residual -122.00 -137.85 15.85 0 2.50e+00 1.60e-01 4.02e+01 dihedral pdb=" N THR D 261 " pdb=" C THR D 261 " pdb=" CA THR D 261 " pdb=" CB THR D 261 " ideal model delta harmonic sigma weight residual 123.40 137.67 -14.27 0 2.50e+00 1.60e-01 3.26e+01 dihedral pdb=" C16 9XX A 602 " pdb=" O 9XX A 602 " pdb=" C15 9XX A 602 " pdb=" O6 9XX A 602 " ideal model delta sinusoidal sigma weight residual -2.46 169.87 -172.33 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 7495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 1978 0.124 - 0.247: 24 0.247 - 0.371: 1 0.371 - 0.495: 0 0.495 - 0.618: 1 Chirality restraints: 2004 Sorted by residual: chirality pdb=" CA THR D 261 " pdb=" N THR D 261 " pdb=" C THR D 261 " pdb=" CB THR D 261 " both_signs ideal model delta sigma weight residual False 2.53 1.91 0.62 2.00e-01 2.50e+01 9.55e+00 chirality pdb=" CA ARG B 7 " pdb=" N ARG B 7 " pdb=" C ARG B 7 " pdb=" CB ARG B 7 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA SER D 259 " pdb=" N SER D 259 " pdb=" C SER D 259 " pdb=" CB SER D 259 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 2001 not shown) Planarity restraints: 2239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 192 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.94e+00 pdb=" C LEU C 192 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU C 192 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG C 193 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 257 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO D 258 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 258 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 258 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 60 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO B 61 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 61 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 61 " -0.036 5.00e-02 4.00e+02 ... (remaining 2236 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2236 2.76 - 3.30: 11537 3.30 - 3.83: 18849 3.83 - 4.37: 22967 4.37 - 4.90: 40319 Nonbonded interactions: 95908 Sorted by model distance: nonbonded pdb=" OH TYR A 70 " pdb=" O LEU A 178 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR A 468 " pdb=" OD2 ASP A 503 " model vdw 2.243 3.040 nonbonded pdb=" NE2 GLN D 160 " pdb=" O PRO D 180 " model vdw 2.250 3.120 nonbonded pdb=" OD1 ASP A 259 " pdb=" OG1 THR B 165 " model vdw 2.262 3.040 nonbonded pdb=" OD2 ASP C 45 " pdb=" OG1 THR C 47 " model vdw 2.313 3.040 ... (remaining 95903 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.070 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.292 12622 Z= 0.335 Angle : 0.724 12.065 17210 Z= 0.410 Chirality : 0.048 0.618 2004 Planarity : 0.005 0.070 2239 Dihedral : 14.237 172.335 4538 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.87 % Favored : 91.00 % Rotamer: Outliers : 0.55 % Allowed : 4.49 % Favored : 94.96 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.18), residues: 1612 helix: -2.61 (0.16), residues: 742 sheet: -2.40 (0.40), residues: 153 loop : -3.34 (0.20), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 12 HIS 0.004 0.001 HIS C 71 PHE 0.013 0.001 PHE A 165 TYR 0.022 0.001 TYR D 354 ARG 0.002 0.000 ARG D 33 Details of bonding type rmsd hydrogen bonds : bond 0.14129 ( 464) hydrogen bonds : angle 6.45991 ( 1353) covalent geometry : bond 0.00412 (12620) covalent geometry : angle 0.72450 (17210) Misc. bond : bond 0.21265 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 1.249 Fit side-chains REVERT: B 28 PHE cc_start: 0.7962 (t80) cc_final: 0.7579 (t80) REVERT: B 68 ARG cc_start: 0.7615 (mmt180) cc_final: 0.7225 (ttm-80) REVERT: C 112 TRP cc_start: 0.7411 (t60) cc_final: 0.6876 (t-100) REVERT: D 404 ARG cc_start: 0.7321 (mmt180) cc_final: 0.7024 (mtm-85) outliers start: 7 outliers final: 2 residues processed: 132 average time/residue: 0.3282 time to fit residues: 57.6831 Evaluate side-chains 94 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain C residue 286 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 81 optimal weight: 0.0060 chunk 64 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 497 GLN B 65 GLN B 152 GLN B 201 ASN ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN C 198 ASN D 103 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.100338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.080764 restraints weight = 20750.718| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.37 r_work: 0.2795 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12622 Z= 0.118 Angle : 0.598 10.919 17210 Z= 0.306 Chirality : 0.043 0.168 2004 Planarity : 0.005 0.068 2239 Dihedral : 8.597 139.989 1835 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 1.02 % Allowed : 8.90 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.20), residues: 1612 helix: -1.53 (0.19), residues: 722 sheet: -1.86 (0.41), residues: 156 loop : -2.72 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 518 HIS 0.004 0.001 HIS C 71 PHE 0.012 0.001 PHE C 7 TYR 0.015 0.001 TYR D 354 ARG 0.013 0.000 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 464) hydrogen bonds : angle 4.83575 ( 1353) covalent geometry : bond 0.00262 (12620) covalent geometry : angle 0.59795 (17210) Misc. bond : bond 0.00105 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 1.235 Fit side-chains REVERT: B 12 MET cc_start: 0.8329 (ttp) cc_final: 0.8119 (ttp) REVERT: B 28 PHE cc_start: 0.7714 (t80) cc_final: 0.7425 (t80) REVERT: B 68 ARG cc_start: 0.7651 (mmt180) cc_final: 0.7086 (ttm-80) REVERT: B 215 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8172 (pp) REVERT: C 13 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7726 (mpt180) REVERT: C 112 TRP cc_start: 0.8000 (t60) cc_final: 0.7063 (t-100) REVERT: C 175 ASP cc_start: 0.8971 (p0) cc_final: 0.8648 (p0) REVERT: C 276 ASP cc_start: 0.8209 (m-30) cc_final: 0.7928 (m-30) REVERT: C 283 ARG cc_start: 0.7826 (ttm170) cc_final: 0.7213 (ttm170) REVERT: D 404 ARG cc_start: 0.7466 (mmt180) cc_final: 0.6915 (mtm-85) REVERT: D 430 ARG cc_start: 0.9094 (ttp80) cc_final: 0.8702 (mtp-110) outliers start: 13 outliers final: 4 residues processed: 122 average time/residue: 0.2698 time to fit residues: 46.3578 Evaluate side-chains 105 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 25 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 115 optimal weight: 0.0770 chunk 117 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.100276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.080727 restraints weight = 21028.366| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.36 r_work: 0.2795 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12622 Z= 0.123 Angle : 0.579 10.945 17210 Z= 0.295 Chirality : 0.043 0.153 2004 Planarity : 0.004 0.066 2239 Dihedral : 8.012 118.444 1830 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.97 % Allowed : 9.06 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.21), residues: 1612 helix: -1.05 (0.19), residues: 728 sheet: -1.40 (0.44), residues: 147 loop : -2.35 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 518 HIS 0.004 0.001 HIS C 71 PHE 0.017 0.001 PHE B 16 TYR 0.015 0.001 TYR D 354 ARG 0.004 0.000 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 464) hydrogen bonds : angle 4.59869 ( 1353) covalent geometry : bond 0.00284 (12620) covalent geometry : angle 0.57916 (17210) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 1.211 Fit side-chains REVERT: A 85 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8088 (tm-30) REVERT: B 12 MET cc_start: 0.8418 (ttp) cc_final: 0.8204 (ttp) REVERT: B 28 PHE cc_start: 0.7564 (t80) cc_final: 0.7289 (t80) REVERT: B 68 ARG cc_start: 0.7635 (mmt180) cc_final: 0.7078 (ttm-80) REVERT: B 176 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8865 (tt) REVERT: B 185 MET cc_start: 0.8440 (tpt) cc_final: 0.7711 (mmm) REVERT: B 215 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8132 (pp) REVERT: C 13 ARG cc_start: 0.7950 (mpt180) cc_final: 0.7573 (mpt180) REVERT: C 112 TRP cc_start: 0.7963 (t60) cc_final: 0.7054 (t-100) REVERT: C 175 ASP cc_start: 0.8941 (p0) cc_final: 0.8554 (p0) REVERT: C 276 ASP cc_start: 0.8254 (m-30) cc_final: 0.7951 (m-30) REVERT: C 283 ARG cc_start: 0.7793 (ttm170) cc_final: 0.7112 (ttm170) REVERT: D 404 ARG cc_start: 0.7442 (mmt180) cc_final: 0.6926 (mtm-85) outliers start: 25 outliers final: 7 residues processed: 128 average time/residue: 0.2609 time to fit residues: 47.2207 Evaluate side-chains 103 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 130 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN B 224 HIS D 363 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.096918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.077378 restraints weight = 21193.498| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.36 r_work: 0.2735 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 12622 Z= 0.239 Angle : 0.656 13.540 17210 Z= 0.335 Chirality : 0.047 0.160 2004 Planarity : 0.005 0.063 2239 Dihedral : 8.081 114.974 1830 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 1.89 % Allowed : 11.42 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.21), residues: 1612 helix: -0.91 (0.19), residues: 727 sheet: -1.22 (0.43), residues: 153 loop : -2.32 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 398 HIS 0.005 0.001 HIS C 71 PHE 0.016 0.002 PHE A 165 TYR 0.023 0.001 TYR D 354 ARG 0.006 0.000 ARG D 361 Details of bonding type rmsd hydrogen bonds : bond 0.04923 ( 464) hydrogen bonds : angle 4.82108 ( 1353) covalent geometry : bond 0.00571 (12620) covalent geometry : angle 0.65643 (17210) Misc. bond : bond 0.00031 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 1.257 Fit side-chains REVERT: A 85 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8085 (tm-30) REVERT: B 28 PHE cc_start: 0.7765 (t80) cc_final: 0.7555 (t80) REVERT: B 68 ARG cc_start: 0.7676 (mmt180) cc_final: 0.7132 (ttm-80) REVERT: B 95 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8237 (t80) REVERT: B 215 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8324 (pp) REVERT: C 112 TRP cc_start: 0.8035 (t60) cc_final: 0.7072 (t-100) REVERT: C 175 ASP cc_start: 0.8925 (p0) cc_final: 0.8568 (p0) REVERT: C 276 ASP cc_start: 0.8301 (m-30) cc_final: 0.8033 (m-30) REVERT: C 283 ARG cc_start: 0.7890 (ttm170) cc_final: 0.7104 (ttm170) REVERT: D 75 ARG cc_start: 0.7777 (mtm110) cc_final: 0.7507 (mtm110) REVERT: D 404 ARG cc_start: 0.7488 (mmt180) cc_final: 0.6992 (mtm-85) outliers start: 24 outliers final: 12 residues processed: 117 average time/residue: 0.2675 time to fit residues: 44.7153 Evaluate side-chains 105 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.099701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.080202 restraints weight = 20976.456| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.34 r_work: 0.2786 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12622 Z= 0.120 Angle : 0.580 11.255 17210 Z= 0.294 Chirality : 0.043 0.182 2004 Planarity : 0.004 0.064 2239 Dihedral : 7.704 112.739 1830 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.81 % Allowed : 12.44 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.21), residues: 1612 helix: -0.64 (0.20), residues: 727 sheet: -1.08 (0.45), residues: 152 loop : -2.13 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 518 HIS 0.004 0.001 HIS C 71 PHE 0.010 0.001 PHE B 16 TYR 0.015 0.001 TYR D 354 ARG 0.004 0.000 ARG D 361 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 464) hydrogen bonds : angle 4.56495 ( 1353) covalent geometry : bond 0.00276 (12620) covalent geometry : angle 0.58033 (17210) Misc. bond : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 1.354 Fit side-chains REVERT: A 85 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8040 (tm-30) REVERT: A 104 ASP cc_start: 0.8396 (t0) cc_final: 0.8193 (t0) REVERT: B 28 PHE cc_start: 0.7537 (t80) cc_final: 0.7312 (t80) REVERT: B 68 ARG cc_start: 0.7636 (mmt180) cc_final: 0.7259 (ttm-80) REVERT: B 95 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8260 (t80) REVERT: B 185 MET cc_start: 0.8474 (tpt) cc_final: 0.7764 (mmm) REVERT: B 215 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8227 (pp) REVERT: C 112 TRP cc_start: 0.7963 (t60) cc_final: 0.7110 (t-100) REVERT: C 175 ASP cc_start: 0.8914 (p0) cc_final: 0.8613 (p0) REVERT: C 276 ASP cc_start: 0.8298 (m-30) cc_final: 0.8033 (m-30) REVERT: D 75 ARG cc_start: 0.7777 (mtm110) cc_final: 0.7510 (mtm110) REVERT: D 404 ARG cc_start: 0.7407 (mmt180) cc_final: 0.6878 (mtm-85) outliers start: 23 outliers final: 12 residues processed: 123 average time/residue: 0.2684 time to fit residues: 47.6093 Evaluate side-chains 108 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 120 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 136 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.097995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.078813 restraints weight = 21260.097| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.32 r_work: 0.2764 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12622 Z= 0.176 Angle : 0.605 11.890 17210 Z= 0.308 Chirality : 0.045 0.152 2004 Planarity : 0.004 0.062 2239 Dihedral : 7.668 111.473 1830 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 1.73 % Allowed : 12.91 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.21), residues: 1612 helix: -0.53 (0.20), residues: 727 sheet: -1.02 (0.45), residues: 151 loop : -2.09 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 518 HIS 0.005 0.001 HIS C 71 PHE 0.013 0.001 PHE A 165 TYR 0.019 0.001 TYR D 354 ARG 0.005 0.000 ARG C 286 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 464) hydrogen bonds : angle 4.61888 ( 1353) covalent geometry : bond 0.00420 (12620) covalent geometry : angle 0.60506 (17210) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 1.215 Fit side-chains REVERT: A 85 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8049 (tm-30) REVERT: A 104 ASP cc_start: 0.8483 (t0) cc_final: 0.8261 (t0) REVERT: B 28 PHE cc_start: 0.7648 (t80) cc_final: 0.7446 (t80) REVERT: B 68 ARG cc_start: 0.7656 (mmt180) cc_final: 0.7294 (ttm-80) REVERT: B 95 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8277 (t80) REVERT: B 185 MET cc_start: 0.8517 (tpt) cc_final: 0.7806 (mmm) REVERT: B 215 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8244 (pp) REVERT: C 112 TRP cc_start: 0.7977 (t60) cc_final: 0.7071 (t-100) REVERT: C 175 ASP cc_start: 0.8916 (p0) cc_final: 0.8575 (p0) REVERT: C 276 ASP cc_start: 0.8397 (m-30) cc_final: 0.8025 (m-30) REVERT: D 75 ARG cc_start: 0.7780 (mtm110) cc_final: 0.7524 (mtm110) REVERT: D 404 ARG cc_start: 0.7396 (mmt180) cc_final: 0.6891 (mtm-85) outliers start: 22 outliers final: 16 residues processed: 115 average time/residue: 0.2710 time to fit residues: 44.2982 Evaluate side-chains 112 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 0.0570 chunk 35 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.100058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.081282 restraints weight = 20878.532| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.28 r_work: 0.2803 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12622 Z= 0.112 Angle : 0.566 10.534 17210 Z= 0.288 Chirality : 0.043 0.185 2004 Planarity : 0.004 0.063 2239 Dihedral : 7.405 111.244 1830 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.57 % Allowed : 13.94 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.21), residues: 1612 helix: -0.33 (0.20), residues: 733 sheet: -0.85 (0.47), residues: 144 loop : -1.94 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 518 HIS 0.004 0.001 HIS C 71 PHE 0.009 0.001 PHE B 16 TYR 0.013 0.001 TYR D 354 ARG 0.007 0.000 ARG C 286 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 464) hydrogen bonds : angle 4.43965 ( 1353) covalent geometry : bond 0.00258 (12620) covalent geometry : angle 0.56611 (17210) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 1.321 Fit side-chains REVERT: A 85 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7618 (mp0) REVERT: A 104 ASP cc_start: 0.8426 (t0) cc_final: 0.8188 (t0) REVERT: B 28 PHE cc_start: 0.7522 (t80) cc_final: 0.7295 (t80) REVERT: B 68 ARG cc_start: 0.7632 (mmt180) cc_final: 0.7280 (ttm-80) REVERT: B 95 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8278 (t80) REVERT: B 185 MET cc_start: 0.8499 (tpt) cc_final: 0.7799 (mmm) REVERT: B 215 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8169 (pp) REVERT: C 112 TRP cc_start: 0.7915 (t60) cc_final: 0.7087 (t-100) REVERT: C 175 ASP cc_start: 0.8856 (p0) cc_final: 0.8597 (p0) REVERT: C 276 ASP cc_start: 0.8380 (m-30) cc_final: 0.7880 (m-30) REVERT: C 283 ARG cc_start: 0.8353 (ttm170) cc_final: 0.7954 (ttm170) REVERT: D 75 ARG cc_start: 0.7718 (mtm110) cc_final: 0.7466 (mtm110) REVERT: D 404 ARG cc_start: 0.7319 (mmt180) cc_final: 0.6848 (mtm-85) REVERT: D 430 ARG cc_start: 0.9144 (ttp80) cc_final: 0.8885 (ptm-80) outliers start: 20 outliers final: 15 residues processed: 119 average time/residue: 0.2781 time to fit residues: 46.7819 Evaluate side-chains 116 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 154 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.098071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.078785 restraints weight = 21400.707| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.34 r_work: 0.2759 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12622 Z= 0.182 Angle : 0.615 12.263 17210 Z= 0.312 Chirality : 0.045 0.256 2004 Planarity : 0.004 0.062 2239 Dihedral : 7.471 109.020 1830 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 1.97 % Allowed : 13.86 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.21), residues: 1612 helix: -0.31 (0.20), residues: 736 sheet: -0.87 (0.46), residues: 149 loop : -1.99 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 398 HIS 0.004 0.001 HIS C 71 PHE 0.013 0.001 PHE A 165 TYR 0.023 0.001 TYR D 354 ARG 0.005 0.000 ARG C 286 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 464) hydrogen bonds : angle 4.58038 ( 1353) covalent geometry : bond 0.00436 (12620) covalent geometry : angle 0.61494 (17210) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 1.280 Fit side-chains REVERT: A 85 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7993 (tm-30) REVERT: A 104 ASP cc_start: 0.8557 (t0) cc_final: 0.8345 (t0) REVERT: B 68 ARG cc_start: 0.7643 (mmt180) cc_final: 0.7277 (ttm-80) REVERT: B 95 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8261 (t80) REVERT: B 185 MET cc_start: 0.8541 (tpt) cc_final: 0.7917 (mpp) REVERT: B 215 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8263 (pp) REVERT: C 112 TRP cc_start: 0.7980 (t60) cc_final: 0.7101 (t-100) REVERT: C 175 ASP cc_start: 0.8879 (p0) cc_final: 0.8545 (p0) REVERT: C 276 ASP cc_start: 0.8402 (m-30) cc_final: 0.8029 (m-30) REVERT: D 75 ARG cc_start: 0.7759 (mtm110) cc_final: 0.7483 (mtm110) REVERT: D 404 ARG cc_start: 0.7252 (mmt180) cc_final: 0.6784 (mtm-85) REVERT: D 430 ARG cc_start: 0.9148 (ttp80) cc_final: 0.8886 (ptm-80) outliers start: 25 outliers final: 19 residues processed: 118 average time/residue: 0.2916 time to fit residues: 47.9389 Evaluate side-chains 121 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 121 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN B 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.099628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.080163 restraints weight = 21014.462| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.35 r_work: 0.2781 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12622 Z= 0.134 Angle : 0.596 12.667 17210 Z= 0.300 Chirality : 0.044 0.200 2004 Planarity : 0.004 0.063 2239 Dihedral : 7.349 108.462 1830 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.73 % Allowed : 14.49 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.21), residues: 1612 helix: -0.16 (0.20), residues: 733 sheet: -0.81 (0.46), residues: 149 loop : -1.93 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 398 HIS 0.004 0.001 HIS C 71 PHE 0.022 0.001 PHE B 28 TYR 0.017 0.001 TYR D 354 ARG 0.007 0.000 ARG D 361 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 464) hydrogen bonds : angle 4.47393 ( 1353) covalent geometry : bond 0.00315 (12620) covalent geometry : angle 0.59590 (17210) Misc. bond : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 1.408 Fit side-chains REVERT: A 85 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7572 (mp0) REVERT: A 104 ASP cc_start: 0.8465 (t0) cc_final: 0.8248 (t0) REVERT: B 68 ARG cc_start: 0.7640 (mmt180) cc_final: 0.7280 (ttm-80) REVERT: B 95 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8257 (t80) REVERT: B 185 MET cc_start: 0.8525 (tpt) cc_final: 0.7911 (mpp) REVERT: B 215 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8214 (pp) REVERT: C 112 TRP cc_start: 0.7949 (t60) cc_final: 0.7105 (t-100) REVERT: C 175 ASP cc_start: 0.8856 (p0) cc_final: 0.8602 (p0) REVERT: C 276 ASP cc_start: 0.8381 (m-30) cc_final: 0.8016 (m-30) REVERT: D 75 ARG cc_start: 0.7718 (mtm110) cc_final: 0.7445 (mtm110) REVERT: D 361 ARG cc_start: 0.7020 (tpm170) cc_final: 0.6726 (tpt170) REVERT: D 404 ARG cc_start: 0.7216 (mmt180) cc_final: 0.6845 (mtm-85) REVERT: D 430 ARG cc_start: 0.9152 (ttp80) cc_final: 0.8908 (ptm-80) outliers start: 22 outliers final: 17 residues processed: 118 average time/residue: 0.3286 time to fit residues: 54.8612 Evaluate side-chains 117 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 122 optimal weight: 0.6980 chunk 58 optimal weight: 0.0060 chunk 44 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 0.0770 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS B 65 GLN B 201 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.102556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.082983 restraints weight = 20745.941| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.36 r_work: 0.2829 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12622 Z= 0.098 Angle : 0.564 13.544 17210 Z= 0.283 Chirality : 0.042 0.168 2004 Planarity : 0.004 0.063 2239 Dihedral : 7.094 109.181 1830 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.26 % Allowed : 14.96 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.22), residues: 1612 helix: 0.09 (0.20), residues: 734 sheet: -0.73 (0.47), residues: 145 loop : -1.75 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 518 HIS 0.004 0.001 HIS C 71 PHE 0.023 0.001 PHE B 28 TYR 0.011 0.001 TYR C 176 ARG 0.007 0.000 ARG C 286 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 464) hydrogen bonds : angle 4.27195 ( 1353) covalent geometry : bond 0.00216 (12620) covalent geometry : angle 0.56429 (17210) Misc. bond : bond 0.00009 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 1.449 Fit side-chains REVERT: A 85 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7551 (mp0) REVERT: B 68 ARG cc_start: 0.7613 (mmt180) cc_final: 0.7230 (ttm-80) REVERT: B 95 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8268 (t80) REVERT: B 185 MET cc_start: 0.8482 (tpt) cc_final: 0.7799 (mmm) REVERT: C 112 TRP cc_start: 0.7904 (t60) cc_final: 0.7113 (t-100) REVERT: C 175 ASP cc_start: 0.8827 (p0) cc_final: 0.8609 (p0) REVERT: C 276 ASP cc_start: 0.8421 (m-30) cc_final: 0.8064 (m-30) REVERT: D 361 ARG cc_start: 0.6850 (tpm170) cc_final: 0.6578 (tpt170) REVERT: D 404 ARG cc_start: 0.7119 (mmt180) cc_final: 0.6811 (mtm-85) REVERT: D 430 ARG cc_start: 0.9154 (ttp80) cc_final: 0.8902 (ptm-80) outliers start: 16 outliers final: 13 residues processed: 125 average time/residue: 0.2944 time to fit residues: 51.5993 Evaluate side-chains 118 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 9 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 141 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 103 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.083352 restraints weight = 20865.918| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.38 r_work: 0.2836 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12622 Z= 0.099 Angle : 0.572 12.918 17210 Z= 0.285 Chirality : 0.042 0.177 2004 Planarity : 0.004 0.063 2239 Dihedral : 6.997 109.913 1830 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.26 % Allowed : 15.28 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.22), residues: 1612 helix: 0.20 (0.20), residues: 736 sheet: -0.67 (0.48), residues: 145 loop : -1.70 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 518 HIS 0.004 0.000 HIS C 71 PHE 0.022 0.001 PHE B 28 TYR 0.011 0.001 TYR C 176 ARG 0.010 0.000 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 464) hydrogen bonds : angle 4.23518 ( 1353) covalent geometry : bond 0.00220 (12620) covalent geometry : angle 0.57152 (17210) Misc. bond : bond 0.00008 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5932.93 seconds wall clock time: 103 minutes 51.43 seconds (6231.43 seconds total)